GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Shewanella sp. ANA-3

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 7025148 Shewana3_2311 alpha amylase, catalytic region (RefSeq)

Query= uniprot:H3K096
         (538 letters)



>FitnessBrowser__ANA3:7025148
          Length = 540

 Score =  643 bits (1659), Expect = 0.0
 Identities = 298/529 (56%), Positives = 376/529 (71%), Gaps = 3/529 (0%)

Query: 5   MMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFG 64
           + WWRG VIYQIYPRS LD+ GDGVGDL GI  KLDY+ASLNVD IW+SPFF SPM DFG
Sbjct: 4   LTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFG 63

Query: 65  YDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPK 124
           YD+SDYR+VDP+FGT++DF  L+EKAH  G+KV+IDQV+SHTSDQH WF ESR++RTNPK
Sbjct: 64  YDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRTNPK 123

Query: 125 ADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQ 184
           ADW+VWA+PK DGT PNNWL+IFGG AW ++ RRQQYYLHNFL SQPD+NFH+P+ RQA 
Sbjct: 124 ADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAV 183

Query: 185 LDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDL 244
           LDN+ FWL  GVDGFRLD + F +HD +LRDNPP PK + +  G  E NPY +Q H Y+ 
Sbjct: 184 LDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHYYNN 243

Query: 245 SRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH 304
            RP+ + F+++LR L++ YPG  T+GE+  ++ L  MA YT G D+LHMAY+F+LL   +
Sbjct: 244 DRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLTDDY 303

Query: 305 SASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGS 364
           SA+Y+R+ +E  +   GD WPCWA  NHD  R A+RWG  +      K++ A++ SLRGS
Sbjct: 304 SAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGRGKQTSDMVKMLNAMVNSLRGS 363

Query: 365 VCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPW 423
           VC YQGEELGL EA + +  +QDP+GK  WP FKGRDGCRTPMPW  + +  GFS V PW
Sbjct: 364 VCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFSGFSQVTPW 423

Query: 424 LPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQK 483
           LP+   H  LAV  Q+ D  + L+  R  LA+R+ +PAL +G++  +D  + LL F R  
Sbjct: 424 LPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEPLLVFVRTS 483

Query: 484 GDETLLCVFNLTGQEQQTTLPVEVASDLPVAH--FTATRDGSTLTLPAY 530
           G++ LL  FNL   EQ  +L           H   TA R   TLT  AY
Sbjct: 484 GEQKLLVCFNLQDTEQALSLDALSIQQEITGHGLKTAQRIADTLTFSAY 532


Lambda     K      H
   0.320    0.138    0.443 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 946
Number of extensions: 40
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 538
Length of database: 540
Length adjustment: 35
Effective length of query: 503
Effective length of database: 505
Effective search space:   254015
Effective search space used:   254015
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory